Researchers use new approach to predict protein function

Jul 11, 2007
Enolase Enzyme
Homology modeled complex (in cyan) of the enolase enzyme, BC0371, with its substrate, N-succinyl-L-arginine, matches very closely the experimentally determined structure (in yellow) via X-ray crystallography. Credit: Image courtesy of John A. Gerlt and Nature Chemical Biology

In a paper published online this month in the journal Nature Chemical Biology, researchers report that they have developed a way to determine the function of some of the hundreds of thousands of proteins for which amino acid sequence data are available, but whose structure and function remain unknown.

The research team, led by University of Illinois biochemistry professor John A. Gerlt, is the first to use a computational approach to accurately predict a protein’s function from its amino acid sequence. Their “in silico” (computer-aided) predictions were validated in the laboratory by means of enzyme assays and X-ray crystallography.

The new approach involved searching databases of known proteins for those with amino acid sequences that had the greatest homology to the unknown proteins. The researchers then used the three-dimensional structures of the most closely matched known proteins in their analyses of protein function.

Using the structural data obtained from this homology modeling, the team performed computerized docking experiments to quickly evaluate whether the unknown proteins were likely to bind to any of a vast library of potential target molecules, or substrates. Determining which substrate binds to a given protein is vital to understanding the protein’s function.

“This study describes an integrated approach using experimental techniques, computational techniques and X-ray crystallography for predicting the function of a protein of previously unknown function,” Gerlt said.

These methods will speed the task of identifying the biological roles of some of the hundreds of thousands of proteins whose functions have not yet been discovered.

“Rather than trying to do (laboratory) experiments on 30,000 compounds to determine if they are substrates, with this approach you might do experiments on 10,” Gerlt said.

The study involved a family of proteins within the large and diverse enolase superfamily. Enolases are enzymes that catalyze the breakdown of glucose and related compounds into other molecules as needed for metabolism.

The enzymes within the enolase superfamily utilize similar reaction mechanisms to one another but catalyze different reactions, complicating the task of discovering their function. There are more than 3,000 proteins in the enolase superfamily, and a majority of them have not yet been fully – or accurately – characterized. (The new study also revealed that one family of enolase proteins had been misclassified.)

Gerlt and his colleagues expect that the computational approach they pioneered will help scientists more efficiently tackle the problem of understanding these – and other – unknown proteins.

“There are 4 1/2 million protein sequences in the sequence databanks, and maybe the functions are known for, can be assigned to, half of those with some reliability,” Gerlt said. “That tells you that there is a lot of biology to be discovered.”

Source: University of Illinois at Urbana-Champaign

Explore further: Compact wool measurement tool may find home on the range

add to favorites email to friend print save as pdf

Related Stories

Solving the Hox Specificity Paradox

Jan 22, 2015

The remarkable diversity of anatomical features along the body axis of animals—the differences between the head, the thorax and the abdomen, for example—is determined by proteins in the Hox family. But ...

New computation method helps identify functional DNA

Jan 21, 2015

Striving to unravel and comprehend DNA's biological significance, Cornell scientists have created a new computational method that can identify positions in the human genome that play a role in the proper ...

Recommended for you

Population genomics unveil seahorse domain

11 hours ago

In a finding vital to effective species management, a team including City College of New York biologists has determined that the lined seahorse (Hippocampus erectus) is more a permanent resident of the we ...

Researchers develop new potato cultivar

14 hours ago

Dakota Ruby is the name of a new potato cultivar developed by the NDSU potato breeding project and released by the North Dakota Agricultural Experiment Station. Dakota Ruby has bright red skin, stores well and is intended ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.